(primary solid tumor cohort)
This pipeline computes the correlation between cancer subtypes identified by different molecular patterns and selected clinical features.
Testing the association between subtypes identified by 8 different clustering approaches and 12 clinical features across 327 patients, 6 significant findings detected with P value < 0.05 and Q value < 0.25.
-
6 subtypes identified in current cancer cohort by 'Copy Number Ratio CNMF subtypes'. These subtypes correlate to 'Time to Death', 'NUMBERPACKYEARSSMOKED', and 'TOBACCOSMOKINGHISTORYINDICATOR'.
-
8 subtypes identified in current cancer cohort by 'METHLYATION CNMF'. These subtypes correlate to 'AGE' and 'TOBACCOSMOKINGHISTORYINDICATOR'.
-
CNMF clustering analysis on RPPA data identified 4 subtypes that correlate to 'GENDER'.
-
Consensus hierarchical clustering analysis on RPPA data identified 3 subtypes that do not correlate to any clinical features.
-
CNMF clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that do not correlate to any clinical features.
-
Consensus hierarchical clustering analysis on sequencing-based mRNA expression data identified 3 subtypes that do not correlate to any clinical features.
-
3 subtypes identified in current cancer cohort by 'MIRSEQ CNMF'. These subtypes do not correlate to any clinical features.
-
3 subtypes identified in current cancer cohort by 'MIRSEQ CHIERARCHICAL'. These subtypes do not correlate to any clinical features.
Clinical Features |
Statistical Tests |
Copy Number Ratio CNMF subtypes |
METHLYATION CNMF |
RPPA CNMF subtypes |
RPPA cHierClus subtypes |
RNAseq CNMF subtypes |
RNAseq cHierClus subtypes |
MIRSEQ CNMF |
MIRSEQ CHIERARCHICAL |
Time to Death | logrank test |
0.000432 (0.0389) |
0.0554 (1.00) |
0.684 (1.00) |
0.137 (1.00) |
0.448 (1.00) |
0.205 (1.00) |
0.101 (1.00) |
0.0949 (1.00) |
AGE | ANOVA |
0.106 (1.00) |
0.000106 (0.00964) |
0.409 (1.00) |
0.274 (1.00) |
0.925 (1.00) |
0.383 (1.00) |
0.551 (1.00) |
0.391 (1.00) |
GENDER | Fisher's exact test |
0.405 (1.00) |
0.0445 (1.00) |
0.00242 (0.208) |
0.973 (1.00) |
0.188 (1.00) |
0.00985 (0.827) |
0.0974 (1.00) |
0.657 (1.00) |
PATHOLOGY T | Chi-square test |
0.0177 (1.00) |
0.0887 (1.00) |
0.113 (1.00) |
0.213 (1.00) |
0.225 (1.00) |
0.298 (1.00) |
0.197 (1.00) |
0.0973 (1.00) |
PATHOLOGY N | Chi-square test |
0.00805 (0.684) |
0.439 (1.00) |
0.146 (1.00) |
0.156 (1.00) |
0.194 (1.00) |
0.0772 (1.00) |
0.124 (1.00) |
0.752 (1.00) |
PATHOLOGICSPREAD(M) | Fisher's exact test |
0.628 (1.00) |
0.494 (1.00) |
1 (1.00) |
|||||
TUMOR STAGE | Chi-square test |
0.0286 (1.00) |
0.272 (1.00) |
0.098 (1.00) |
0.192 (1.00) |
0.0364 (1.00) |
0.39 (1.00) |
0.455 (1.00) |
0.0668 (1.00) |
RADIATIONS RADIATION REGIMENINDICATION | Fisher's exact test |
0.32 (1.00) |
0.715 (1.00) |
0.154 (1.00) |
0.611 (1.00) |
0.413 (1.00) |
0.546 (1.00) |
0.787 (1.00) |
0.903 (1.00) |
NUMBERPACKYEARSSMOKED | ANOVA |
0.000531 (0.0462) |
0.0491 (1.00) |
0.0668 (1.00) |
0.654 (1.00) |
0.0646 (1.00) |
0.0544 (1.00) |
0.657 (1.00) |
0.515 (1.00) |
TOBACCOSMOKINGHISTORYINDICATOR | Chi-square test |
0.000469 (0.0418) |
0.00052 (0.0457) |
0.704 (1.00) |
0.186 (1.00) |
0.42 (1.00) |
0.129 (1.00) |
0.326 (1.00) |
0.479 (1.00) |
YEAROFTOBACCOSMOKINGONSET | ANOVA |
0.114 (1.00) |
0.0163 (1.00) |
0.534 (1.00) |
0.709 (1.00) |
0.133 (1.00) |
0.125 (1.00) |
0.409 (1.00) |
0.205 (1.00) |
NUMBER OF LYMPH NODES | ANOVA |
0.155 (1.00) |
0.0311 (1.00) |
0.105 (1.00) |
0.624 (1.00) |
0.175 (1.00) |
0.366 (1.00) |
0.512 (1.00) |
0.496 (1.00) |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 |
---|---|---|---|---|---|---|
Number of samples | 74 | 39 | 46 | 81 | 71 | 10 |
P value = 0.000432 (logrank test), Q value = 0.039
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 317 | 121 | 0.1 - 210.9 (14.0) |
subtype1 | 73 | 35 | 0.2 - 142.5 (13.6) |
subtype2 | 38 | 12 | 0.1 - 111.1 (14.7) |
subtype3 | 46 | 22 | 1.0 - 129.2 (14.1) |
subtype4 | 81 | 18 | 0.8 - 210.9 (21.5) |
subtype5 | 69 | 28 | 0.1 - 126.1 (12.5) |
subtype6 | 10 | 6 | 1.5 - 54.9 (10.2) |
P value = 0.106 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 320 | 61.1 (12.1) |
subtype1 | 73 | 61.8 (11.6) |
subtype2 | 39 | 57.7 (12.6) |
subtype3 | 46 | 63.3 (9.5) |
subtype4 | 81 | 62.1 (12.7) |
subtype5 | 71 | 60.8 (12.6) |
subtype6 | 10 | 53.8 (11.9) |
P value = 0.405 (Chi-square test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 90 | 231 |
subtype1 | 19 | 55 |
subtype2 | 12 | 27 |
subtype3 | 9 | 37 |
subtype4 | 25 | 56 |
subtype5 | 24 | 47 |
subtype6 | 1 | 9 |
P value = 0.0177 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 28 | 81 | 65 | 104 |
subtype1 | 7 | 13 | 14 | 27 |
subtype2 | 2 | 15 | 7 | 10 |
subtype3 | 0 | 9 | 17 | 13 |
subtype4 | 11 | 25 | 11 | 19 |
subtype5 | 8 | 17 | 14 | 29 |
subtype6 | 0 | 2 | 2 | 6 |
P value = 0.00805 (Chi-square test), Q value = 0.68
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 107 | 36 | 99 | 5 |
subtype1 | 15 | 5 | 34 | 2 |
subtype2 | 13 | 5 | 12 | 1 |
subtype3 | 14 | 4 | 15 | 1 |
subtype4 | 35 | 8 | 13 | 0 |
subtype5 | 28 | 13 | 20 | 0 |
subtype6 | 2 | 1 | 5 | 1 |
P value = 0.628 (Chi-square test), Q value = 1
nPatients | M0 | MX |
---|---|---|
ALL | 59 | 6 |
subtype1 | 9 | 2 |
subtype2 | 5 | 1 |
subtype3 | 6 | 1 |
subtype4 | 21 | 1 |
subtype5 | 18 | 1 |
subtype6 | 0 | 0 |
P value = 0.0286 (Chi-square test), Q value = 1
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 20 | 51 | 45 | 157 |
subtype1 | 6 | 5 | 5 | 44 |
subtype2 | 1 | 7 | 7 | 19 |
subtype3 | 0 | 7 | 11 | 21 |
subtype4 | 6 | 15 | 14 | 27 |
subtype5 | 7 | 15 | 8 | 38 |
subtype6 | 0 | 2 | 0 | 8 |
P value = 0.32 (Chi-square test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 76 | 245 |
subtype1 | 22 | 52 |
subtype2 | 10 | 29 |
subtype3 | 11 | 35 |
subtype4 | 20 | 61 |
subtype5 | 13 | 58 |
subtype6 | 0 | 10 |
P value = 0.000531 (ANOVA), Q value = 0.046
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 175 | 50.8 (41.1) |
subtype1 | 49 | 60.3 (49.6) |
subtype2 | 20 | 39.8 (18.1) |
subtype3 | 27 | 73.8 (31.4) |
subtype4 | 43 | 34.6 (23.3) |
subtype5 | 29 | 49.9 (53.8) |
subtype6 | 7 | 29.6 (27.5) |
P value = 0.000469 (Chi-square test), Q value = 0.042
nPatients | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER |
---|---|---|---|---|
ALL | 84 | 57 | 103 | 66 |
subtype1 | 19 | 13 | 35 | 5 |
subtype2 | 8 | 6 | 11 | 13 |
subtype3 | 19 | 4 | 18 | 3 |
subtype4 | 19 | 19 | 19 | 23 |
subtype5 | 17 | 12 | 16 | 21 |
subtype6 | 2 | 3 | 4 | 1 |
P value = 0.114 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 182 | 1965.1 (12.4) |
subtype1 | 51 | 1964.8 (11.9) |
subtype2 | 18 | 1968.6 (6.7) |
subtype3 | 26 | 1960.7 (10.2) |
subtype4 | 46 | 1963.8 (14.8) |
subtype5 | 32 | 1966.8 (12.6) |
subtype6 | 9 | 1972.3 (12.2) |
P value = 0.155 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 242 | 2.6 (5.2) |
subtype1 | 56 | 4.1 (6.8) |
subtype2 | 33 | 2.2 (5.3) |
subtype3 | 38 | 2.7 (6.8) |
subtype4 | 49 | 1.3 (2.4) |
subtype5 | 56 | 2.4 (3.9) |
subtype6 | 10 | 2.8 (3.6) |
Cluster Labels | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 |
---|---|---|---|---|---|---|---|---|
Number of samples | 43 | 47 | 40 | 44 | 58 | 53 | 5 | 19 |
P value = 0.0554 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 306 | 121 | 0.1 - 210.9 (14.6) |
subtype1 | 43 | 15 | 0.1 - 142.5 (13.2) |
subtype2 | 47 | 19 | 0.2 - 126.1 (13.6) |
subtype3 | 39 | 20 | 0.1 - 156.5 (12.7) |
subtype4 | 44 | 8 | 0.8 - 95.0 (22.3) |
subtype5 | 58 | 30 | 0.5 - 135.3 (14.4) |
subtype6 | 51 | 19 | 1.5 - 210.9 (14.3) |
subtype7 | 5 | 1 | 5.0 - 28.6 (10.7) |
subtype8 | 19 | 9 | 1.0 - 84.5 (18.0) |
P value = 0.000106 (ANOVA), Q value = 0.0096
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 309 | 61.1 (12.1) |
subtype1 | 43 | 58.0 (10.6) |
subtype2 | 47 | 55.5 (13.8) |
subtype3 | 40 | 62.4 (11.1) |
subtype4 | 44 | 58.1 (10.9) |
subtype5 | 58 | 64.4 (10.1) |
subtype6 | 53 | 63.9 (13.2) |
subtype7 | 5 | 63.8 (11.7) |
subtype8 | 19 | 67.4 (10.3) |
P value = 0.0445 (Chi-square test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 85 | 224 |
subtype1 | 7 | 36 |
subtype2 | 17 | 30 |
subtype3 | 15 | 25 |
subtype4 | 5 | 39 |
subtype5 | 15 | 43 |
subtype6 | 18 | 35 |
subtype7 | 1 | 4 |
subtype8 | 7 | 12 |
P value = 0.0887 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 24 | 78 | 63 | 102 |
subtype1 | 2 | 10 | 11 | 17 |
subtype2 | 7 | 14 | 12 | 10 |
subtype3 | 1 | 10 | 5 | 19 |
subtype4 | 4 | 9 | 5 | 8 |
subtype5 | 1 | 13 | 13 | 23 |
subtype6 | 8 | 18 | 8 | 17 |
subtype7 | 1 | 0 | 2 | 1 |
subtype8 | 0 | 4 | 7 | 7 |
P value = 0.439 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 101 | 32 | 100 | 5 |
subtype1 | 21 | 4 | 11 | 1 |
subtype2 | 19 | 4 | 14 | 0 |
subtype3 | 15 | 4 | 9 | 2 |
subtype4 | 9 | 5 | 9 | 0 |
subtype5 | 12 | 5 | 24 | 2 |
subtype6 | 18 | 8 | 22 | 0 |
subtype7 | 1 | 0 | 3 | 0 |
subtype8 | 6 | 2 | 8 | 0 |
P value = 0.715 (Chi-square test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 78 | 231 |
subtype1 | 7 | 36 |
subtype2 | 10 | 37 |
subtype3 | 11 | 29 |
subtype4 | 10 | 34 |
subtype5 | 16 | 42 |
subtype6 | 17 | 36 |
subtype7 | 2 | 3 |
subtype8 | 5 | 14 |
P value = 0.0491 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 168 | 49.5 (37.2) |
subtype1 | 29 | 56.3 (30.5) |
subtype2 | 15 | 33.5 (20.9) |
subtype3 | 18 | 55.2 (64.5) |
subtype4 | 22 | 41.8 (44.6) |
subtype5 | 36 | 64.1 (33.8) |
subtype6 | 31 | 42.9 (25.7) |
subtype7 | 4 | 47.2 (23.6) |
subtype8 | 13 | 34.2 (21.4) |
P value = 0.00052 (Chi-square test), Q value = 1
nPatients | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER |
---|---|---|---|---|
ALL | 82 | 55 | 99 | 62 |
subtype1 | 12 | 7 | 21 | 2 |
subtype2 | 7 | 10 | 9 | 18 |
subtype3 | 9 | 6 | 11 | 11 |
subtype4 | 14 | 6 | 11 | 13 |
subtype5 | 23 | 8 | 21 | 3 |
subtype6 | 8 | 14 | 17 | 13 |
subtype7 | 3 | 0 | 2 | 0 |
subtype8 | 6 | 4 | 7 | 2 |
P value = 0.0163 (ANOVA), Q value = 0.046
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 175 | 1964.6 (12.1) |
subtype1 | 25 | 1965.2 (9.2) |
subtype2 | 18 | 1971.8 (12.9) |
subtype3 | 19 | 1967.8 (11.9) |
subtype4 | 26 | 1965.3 (11.8) |
subtype5 | 36 | 1962.4 (11.1) |
subtype6 | 34 | 1964.2 (12.4) |
subtype7 | 5 | 1963.4 (11.3) |
subtype8 | 12 | 1954.9 (14.8) |
P value = 0.0311 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 233 | 2.7 (5.3) |
subtype1 | 36 | 1.5 (2.8) |
subtype2 | 36 | 1.6 (2.2) |
subtype3 | 32 | 2.8 (5.0) |
subtype4 | 18 | 2.1 (2.5) |
subtype5 | 45 | 5.3 (9.9) |
subtype6 | 44 | 2.2 (2.7) |
subtype7 | 4 | 2.2 (2.6) |
subtype8 | 18 | 2.4 (3.0) |
Cluster Labels | 1 | 2 | 3 | 4 |
---|---|---|---|---|
Number of samples | 73 | 52 | 29 | 58 |
P value = 0.684 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 212 | 107 | 0.1 - 210.9 (13.2) |
subtype1 | 73 | 40 | 1.5 - 156.5 (13.2) |
subtype2 | 52 | 23 | 1.4 - 135.3 (11.8) |
subtype3 | 29 | 14 | 2.5 - 114.9 (21.8) |
subtype4 | 58 | 30 | 0.1 - 210.9 (13.2) |
P value = 0.409 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 212 | 62.1 (12.2) |
subtype1 | 73 | 60.2 (13.0) |
subtype2 | 52 | 63.4 (10.0) |
subtype3 | 29 | 63.4 (11.4) |
subtype4 | 58 | 62.8 (13.4) |
P value = 0.00242 (Fisher's exact test), Q value = 0.21
nPatients | FEMALE | MALE |
---|---|---|
ALL | 62 | 150 |
subtype1 | 21 | 52 |
subtype2 | 6 | 46 |
subtype3 | 13 | 16 |
subtype4 | 22 | 36 |
P value = 0.113 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 13 | 59 | 53 | 79 |
subtype1 | 3 | 26 | 13 | 28 |
subtype2 | 4 | 5 | 17 | 22 |
subtype3 | 3 | 10 | 7 | 8 |
subtype4 | 3 | 18 | 16 | 21 |
P value = 0.146 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 73 | 20 | 79 | 4 |
subtype1 | 28 | 8 | 22 | 1 |
subtype2 | 14 | 2 | 27 | 1 |
subtype3 | 15 | 3 | 6 | 1 |
subtype4 | 16 | 7 | 24 | 1 |
P value = 0.154 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 56 | 156 |
subtype1 | 20 | 53 |
subtype2 | 17 | 35 |
subtype3 | 3 | 26 |
subtype4 | 16 | 42 |
P value = 0.0668 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 105 | 48.9 (38.6) |
subtype1 | 33 | 42.7 (27.9) |
subtype2 | 29 | 59.8 (35.1) |
subtype3 | 15 | 61.9 (68.9) |
subtype4 | 28 | 38.0 (26.2) |
P value = 0.704 (Chi-square test), Q value = 1
nPatients | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER |
---|---|---|---|---|
ALL | 60 | 38 | 64 | 40 |
subtype1 | 21 | 10 | 22 | 16 |
subtype2 | 15 | 8 | 18 | 8 |
subtype3 | 9 | 4 | 8 | 7 |
subtype4 | 15 | 16 | 16 | 9 |
P value = 0.534 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 115 | 1964.2 (12.4) |
subtype1 | 38 | 1964.6 (15.5) |
subtype2 | 30 | 1963.1 (9.9) |
subtype3 | 15 | 1968.3 (8.3) |
subtype4 | 32 | 1962.9 (12.2) |
P value = 0.105 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 172 | 2.8 (5.1) |
subtype1 | 55 | 2.4 (3.7) |
subtype2 | 46 | 4.0 (6.0) |
subtype3 | 23 | 1.0 (1.5) |
subtype4 | 48 | 3.2 (6.3) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 116 | 78 | 18 |
P value = 0.137 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 212 | 107 | 0.1 - 210.9 (13.2) |
subtype1 | 116 | 56 | 0.1 - 210.9 (14.2) |
subtype2 | 78 | 41 | 1.5 - 156.5 (13.1) |
subtype3 | 18 | 10 | 3.3 - 52.3 (11.0) |
P value = 0.274 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 212 | 62.1 (12.2) |
subtype1 | 116 | 63.3 (11.2) |
subtype2 | 78 | 60.8 (13.3) |
subtype3 | 18 | 59.9 (13.6) |
P value = 0.973 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 62 | 150 |
subtype1 | 35 | 81 |
subtype2 | 22 | 56 |
subtype3 | 5 | 13 |
P value = 0.213 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 13 | 59 | 53 | 79 |
subtype1 | 8 | 27 | 36 | 40 |
subtype2 | 4 | 28 | 12 | 31 |
subtype3 | 1 | 4 | 5 | 8 |
P value = 0.156 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 73 | 20 | 79 | 4 |
subtype1 | 41 | 8 | 44 | 3 |
subtype2 | 30 | 9 | 24 | 1 |
subtype3 | 2 | 3 | 11 | 0 |
P value = 0.611 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 56 | 156 |
subtype1 | 28 | 88 |
subtype2 | 22 | 56 |
subtype3 | 6 | 12 |
P value = 0.654 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 105 | 48.9 (38.6) |
subtype1 | 61 | 50.1 (45.2) |
subtype2 | 35 | 44.7 (27.3) |
subtype3 | 9 | 56.9 (27.0) |
P value = 0.186 (Chi-square test), Q value = 1
nPatients | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER |
---|---|---|---|---|
ALL | 60 | 38 | 64 | 40 |
subtype1 | 35 | 27 | 32 | 18 |
subtype2 | 21 | 10 | 23 | 18 |
subtype3 | 4 | 1 | 9 | 4 |
P value = 0.709 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 115 | 1964.2 (12.4) |
subtype1 | 67 | 1963.5 (11.1) |
subtype2 | 39 | 1964.9 (15.4) |
subtype3 | 9 | 1966.8 (7.5) |
P value = 0.624 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 172 | 2.8 (5.1) |
subtype1 | 96 | 3.2 (6.1) |
subtype2 | 59 | 2.3 (3.6) |
subtype3 | 17 | 2.7 (3.2) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 118 | 93 | 91 |
P value = 0.448 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 299 | 120 | 0.1 - 210.9 (14.8) |
subtype1 | 118 | 42 | 0.1 - 135.3 (14.2) |
subtype2 | 91 | 40 | 0.2 - 142.5 (15.7) |
subtype3 | 90 | 38 | 0.1 - 210.9 (14.0) |
P value = 0.925 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 302 | 61.0 (12.2) |
subtype1 | 118 | 61.3 (11.1) |
subtype2 | 93 | 60.6 (12.8) |
subtype3 | 91 | 61.2 (12.9) |
P value = 0.188 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 81 | 221 |
subtype1 | 25 | 93 |
subtype2 | 27 | 66 |
subtype3 | 29 | 62 |
P value = 0.225 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 23 | 78 | 60 | 101 |
subtype1 | 6 | 25 | 24 | 36 |
subtype2 | 13 | 25 | 19 | 29 |
subtype3 | 4 | 28 | 17 | 36 |
P value = 0.194 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 100 | 32 | 97 | 5 |
subtype1 | 34 | 10 | 32 | 3 |
subtype2 | 28 | 10 | 42 | 1 |
subtype3 | 38 | 12 | 23 | 1 |
P value = 0.413 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 75 | 227 |
subtype1 | 25 | 93 |
subtype2 | 27 | 66 |
subtype3 | 23 | 68 |
P value = 0.0646 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 165 | 50.0 (37.4) |
subtype1 | 75 | 56.7 (36.5) |
subtype2 | 41 | 48.5 (50.4) |
subtype3 | 49 | 40.9 (21.1) |
P value = 0.42 (Chi-square test), Q value = 1
nPatients | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER |
---|---|---|---|---|
ALL | 82 | 53 | 98 | 58 |
subtype1 | 37 | 17 | 42 | 17 |
subtype2 | 24 | 16 | 29 | 21 |
subtype3 | 21 | 20 | 27 | 20 |
P value = 0.133 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 173 | 1964.5 (12.1) |
subtype1 | 73 | 1963.0 (11.0) |
subtype2 | 49 | 1967.4 (11.5) |
subtype3 | 51 | 1964.1 (13.8) |
P value = 0.175 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 230 | 2.7 (5.3) |
subtype1 | 72 | 2.9 (6.5) |
subtype2 | 83 | 3.3 (5.6) |
subtype3 | 75 | 1.7 (3.2) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 97 | 85 | 120 |
P value = 0.205 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 299 | 120 | 0.1 - 210.9 (14.8) |
subtype1 | 95 | 43 | 1.5 - 142.5 (15.1) |
subtype2 | 84 | 36 | 0.1 - 210.9 (14.0) |
subtype3 | 120 | 41 | 0.1 - 135.3 (15.1) |
P value = 0.383 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 302 | 61.0 (12.2) |
subtype1 | 97 | 60.0 (13.3) |
subtype2 | 85 | 62.5 (12.9) |
subtype3 | 120 | 60.9 (10.5) |
P value = 0.00985 (Fisher's exact test), Q value = 0.83
nPatients | FEMALE | MALE |
---|---|---|
ALL | 81 | 221 |
subtype1 | 31 | 66 |
subtype2 | 29 | 56 |
subtype3 | 21 | 99 |
P value = 0.298 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 23 | 78 | 60 | 101 |
subtype1 | 13 | 27 | 22 | 30 |
subtype2 | 4 | 26 | 15 | 32 |
subtype3 | 6 | 25 | 23 | 39 |
P value = 0.0772 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 100 | 32 | 97 | 5 |
subtype1 | 27 | 12 | 45 | 1 |
subtype2 | 37 | 10 | 20 | 1 |
subtype3 | 36 | 10 | 32 | 3 |
P value = 0.546 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 75 | 227 |
subtype1 | 28 | 69 |
subtype2 | 20 | 65 |
subtype3 | 27 | 93 |
P value = 0.0544 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 165 | 50.0 (37.4) |
subtype1 | 44 | 46.6 (49.1) |
subtype2 | 42 | 40.5 (20.5) |
subtype3 | 79 | 56.9 (35.8) |
P value = 0.129 (Chi-square test), Q value = 1
nPatients | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER |
---|---|---|---|---|
ALL | 82 | 53 | 98 | 58 |
subtype1 | 24 | 19 | 29 | 23 |
subtype2 | 21 | 17 | 22 | 20 |
subtype3 | 37 | 17 | 47 | 15 |
P value = 0.125 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 173 | 1964.5 (12.1) |
subtype1 | 51 | 1967.4 (11.8) |
subtype2 | 44 | 1963.9 (14.2) |
subtype3 | 78 | 1963.0 (10.8) |
P value = 0.366 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 230 | 2.7 (5.3) |
subtype1 | 85 | 3.1 (5.4) |
subtype2 | 68 | 1.9 (3.7) |
subtype3 | 77 | 2.8 (6.3) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 98 | 127 | 100 |
P value = 0.101 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 321 | 123 | 0.1 - 210.9 (14.3) |
subtype1 | 96 | 30 | 0.1 - 210.9 (12.7) |
subtype2 | 127 | 50 | 0.1 - 142.5 (14.0) |
subtype3 | 98 | 43 | 1.0 - 100.5 (17.0) |
P value = 0.551 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 324 | 61.2 (12.1) |
subtype1 | 97 | 61.3 (11.6) |
subtype2 | 127 | 61.9 (11.4) |
subtype3 | 100 | 60.1 (13.3) |
P value = 0.0974 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 92 | 233 |
subtype1 | 22 | 76 |
subtype2 | 34 | 93 |
subtype3 | 36 | 64 |
P value = 0.197 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 28 | 83 | 65 | 106 |
subtype1 | 8 | 29 | 14 | 32 |
subtype2 | 7 | 25 | 28 | 45 |
subtype3 | 13 | 29 | 23 | 29 |
P value = 0.124 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 106 | 36 | 103 | 5 |
subtype1 | 36 | 10 | 24 | 2 |
subtype2 | 43 | 10 | 39 | 3 |
subtype3 | 27 | 16 | 40 | 0 |
P value = 0.494 (Fisher's exact test), Q value = 1
nPatients | M0 | MX |
---|---|---|
ALL | 59 | 6 |
subtype1 | 16 | 3 |
subtype2 | 21 | 1 |
subtype3 | 22 | 2 |
P value = 0.455 (Chi-square test), Q value = 1
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 20 | 51 | 44 | 162 |
subtype1 | 7 | 19 | 10 | 44 |
subtype2 | 4 | 17 | 18 | 65 |
subtype3 | 9 | 15 | 16 | 53 |
P value = 0.787 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 77 | 248 |
subtype1 | 23 | 75 |
subtype2 | 28 | 99 |
subtype3 | 26 | 74 |
P value = 0.657 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 179 | 50.6 (40.9) |
subtype1 | 62 | 49.6 (40.4) |
subtype2 | 73 | 53.7 (36.3) |
subtype3 | 44 | 46.7 (48.6) |
P value = 0.326 (Chi-square test), Q value = 1
nPatients | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER |
---|---|---|---|---|
ALL | 85 | 58 | 105 | 66 |
subtype1 | 27 | 17 | 34 | 18 |
subtype2 | 36 | 19 | 44 | 21 |
subtype3 | 22 | 22 | 27 | 27 |
P value = 0.409 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 186 | 1965.0 (12.3) |
subtype1 | 60 | 1964.7 (12.9) |
subtype2 | 72 | 1963.8 (11.7) |
subtype3 | 54 | 1966.8 (12.4) |
P value = 0.512 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 2.6 (5.2) |
subtype1 | 71 | 2.0 (3.3) |
subtype2 | 90 | 2.7 (6.1) |
subtype3 | 84 | 3.0 (5.5) |
Cluster Labels | 1 | 2 | 3 |
---|---|---|---|
Number of samples | 9 | 124 | 192 |
P value = 0.0949 (logrank test), Q value = 1
nPatients | nDeath | Duration Range (Median), Month | |
---|---|---|---|
ALL | 321 | 123 | 0.1 - 210.9 (14.3) |
subtype1 | 9 | 5 | 3.5 - 56.7 (9.7) |
subtype2 | 122 | 50 | 0.2 - 129.2 (16.0) |
subtype3 | 190 | 68 | 0.1 - 210.9 (14.0) |
P value = 0.391 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 324 | 61.2 (12.1) |
subtype1 | 9 | 59.7 (16.2) |
subtype2 | 124 | 60.1 (12.7) |
subtype3 | 191 | 61.9 (11.4) |
P value = 0.657 (Fisher's exact test), Q value = 1
nPatients | FEMALE | MALE |
---|---|---|
ALL | 92 | 233 |
subtype1 | 2 | 7 |
subtype2 | 39 | 85 |
subtype3 | 51 | 141 |
P value = 0.0973 (Chi-square test), Q value = 1
nPatients | T1 | T2 | T3 | T4 |
---|---|---|---|---|
ALL | 28 | 83 | 65 | 106 |
subtype1 | 0 | 5 | 1 | 3 |
subtype2 | 18 | 32 | 27 | 38 |
subtype3 | 10 | 46 | 37 | 65 |
P value = 0.752 (Chi-square test), Q value = 1
nPatients | N0 | N1 | N2 | N3 |
---|---|---|---|---|
ALL | 106 | 36 | 103 | 5 |
subtype1 | 3 | 1 | 4 | 0 |
subtype2 | 40 | 15 | 48 | 1 |
subtype3 | 63 | 20 | 51 | 4 |
P value = 1 (Fisher's exact test), Q value = 1
nPatients | M0 | MX |
---|---|---|
ALL | 59 | 6 |
subtype1 | 0 | 0 |
subtype2 | 28 | 3 |
subtype3 | 31 | 3 |
P value = 0.0668 (Chi-square test), Q value = 1
nPatients | I | II | III | IV |
---|---|---|---|---|
ALL | 20 | 51 | 44 | 162 |
subtype1 | 0 | 4 | 1 | 4 |
subtype2 | 14 | 18 | 16 | 66 |
subtype3 | 6 | 29 | 27 | 92 |
P value = 0.903 (Fisher's exact test), Q value = 1
nPatients | NO | YES |
---|---|---|
ALL | 77 | 248 |
subtype1 | 2 | 7 |
subtype2 | 31 | 93 |
subtype3 | 44 | 148 |
P value = 0.515 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 179 | 50.6 (40.9) |
subtype1 | 5 | 59.9 (28.9) |
subtype2 | 58 | 45.8 (43.5) |
subtype3 | 116 | 52.6 (40.0) |
P value = 0.479 (Chi-square test), Q value = 1
nPatients | CURRENT REFORMED SMOKER FOR < OR = 15 YEARS | CURRENT REFORMED SMOKER FOR > 15 YEARS | CURRENT SMOKER | LIFELONG NON-SMOKER |
---|---|---|---|---|
ALL | 85 | 58 | 105 | 66 |
subtype1 | 1 | 2 | 4 | 2 |
subtype2 | 30 | 25 | 35 | 31 |
subtype3 | 54 | 31 | 66 | 33 |
P value = 0.205 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 186 | 1965.0 (12.3) |
subtype1 | 4 | 1966.5 (12.0) |
subtype2 | 66 | 1967.1 (12.2) |
subtype3 | 116 | 1963.7 (12.3) |
P value = 0.496 (ANOVA), Q value = 1
nPatients | Mean (Std.Dev) | |
---|---|---|
ALL | 245 | 2.6 (5.2) |
subtype1 | 5 | 5.2 (5.5) |
subtype2 | 107 | 2.7 (4.9) |
subtype3 | 133 | 2.4 (5.4) |
-
Cluster data file = HNSC-TP.mergedcluster.txt
-
Clinical data file = HNSC-TP.clin.merged.picked.txt
-
Number of patients = 327
-
Number of clustering approaches = 8
-
Number of selected clinical features = 12
-
Exclude small clusters that include fewer than K patients, K = 3
consensus non-negative matrix factorization clustering approach (Brunet et al. 2004)
Resampling-based clustering method (Monti et al. 2003)
For survival clinical features, the Kaplan-Meier survival curves of tumors with and without gene mutations were plotted and the statistical significance P values were estimated by logrank test (Bland and Altman 2004) using the 'survdiff' function in R
For continuous numerical clinical features, one-way analysis of variance (Howell 2002) was applied to compare the clinical values between tumor subtypes using 'anova' function in R
For multi-class clinical features (nominal or ordinal), Chi-square tests (Greenwood and Nikulin 1996) were used to estimate the P values using the 'chisq.test' function in R
For binary clinical features, two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R
For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.
This is an experimental feature. The full results of the analysis summarized in this report can be downloaded from the TCGA Data Coordination Center.